We have used both in vitro cell culture systems and non-human primate ocular infection models to better understand chlamydial pathogenesis. These studies have identified chlamydial induced host proteins that are tyrosine phosphorylated in a strain specific manner that implicate differences in chlamydial co-receptor usage during pathogen entry. We also have identified by functional comparative genomic studies of trachoma strains a small subset of genes that correlate with chlamydial strain pathogenic diversity.[unreadable] [unreadable] Chlamydia trachomatis is an obligate intracellular pathogen of humans that exhibits species-specific biological characteristics in its early interactions with host cells that are likely important to pathogenesis. One such characteristic is the tyrosine phosphorylation (Tyr-P) of a circa 70 kDa polypeptide that occurs only following infection of mammalian cells by human isolates/strains. We sought to identify this protein because of its potential significance to the pathogenesis of human chlamydial infections. Using an immunoproteomic approach we identified the host protein ezrin, a member of the ezrin/radixin/moesin (ERM) protein family that serves as a physical link between host cell receptors and the actin cytoskeleton. Confocal microscopy studies showed colocalization of ezrin and actin at the tips and crypts of microvilli, the site of chlamydial attachment and entry, respectively. To demonstrate a functional role for ezrin, we infected cells with a dominant negative (DN) ezrin phenotype, or treated cells with ezrin-specific siRNA. We found that both DN and siRNA-treated cells were significantly less susceptible to infection by human chlamydial strains. Moreover, we demonstrated that inhibition of infection in ezrin DN cells occurred at the stage of chlamydial entry. We hypothesize that the C. trachomatis-specific Tyr-P of ezrin might relate to an undefined species-specific mechanism of pathogen entry that involves chlamydial specific ligand(s) and host cell co-receptor usage.[unreadable] [unreadable] Chlamydia trachomatis is the etiological agent of trachoma, the leading cause of preventable blindness. Trachoma presents distinct clinical syndromes ranging from mild and self-limiting to severe inflammatory disease. The underlying host and pathogen factors responsible for these diverse clinical outcomes are unclear. To assess the role of pathogen variation in disease outcome we analyzed the genomes of four trachoma strains representative of the three major trachoma serotypes using microarray based comparative genome sequencing. Outside of ompA trachoma strains differed primarily in a very small subset (twenty-two) of genes. These subtle genetic variations were manifested in profound differences in virulence as measured by in vitro growth rate, burst size, plaque morphology, and interferon-gamma sensitivity but most importantly in virulence as shown by ocular infection of non-human primates. These findings are the first to identify genes that correlate with different trachoma strain pathogenicities.